From: Michael Mazack (michael_at_mazack.org)
Date: Wed Feb 06 2013 - 09:00:43 CST
Just to follow up on yesterday's discussion, the CVS source-tree now seems
to build without issue. Thank you.
On Tue, Feb 5, 2013 at 2:24 PM, Michael Mazack <michael_at_mazack.org> wrote:
> Thanks for the reply. When I checkout namd2 from CVS (cvs.ks.uiuc.edu) I
> don't currently see the update -- I'll try again tomorrow, as perhaps there
> is some delay somewhere or things are still being checked-in/merged.
> Though, I've also noticed that GCC is giving an error from flipdcd.c and
> sortreplicas.c related to calling exit() and free(). Having these files
> directly include stdlib.h fixes that problem.
> On Tue, Feb 5, 2013 at 1:20 PM, Chris Harrison <charris5_at_gmail.com> wrote:
>> Yes, we discovered the scope bug last night; the gcc compiler complains
>> while the intel does not. It's been fixed and should be available in CVS,
>> and in the nightly build tonight.
>> Let us know if you continue to have problems.
>> On Tue, Feb 5, 2013 at 12:52 PM, Michael Mazack <michael_at_mazack.org>wrote:
>>> Hi. I ran a CVS checkout on the namd2 source-tree yesterday, tried to
>>> rebuild and was given a compiling error:
>>> g++ -m64 -O3
>>> -DCMK_OPTIMIZE=1 -Isrc -Iinc -Iplugins/include -DSTATIC_PLUGIN
>>> -I.rootdir/tcl-threaded/include -DNAMD_TCL -I.rootdir/fftw/include
>>> -DNAMD_FFTW -DNAMD_VERSION=\"2.9\"
>>> -DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE
>>> -DUSE_NODEPATCHMGR -fexpensive-optimizations -ffast-math -o
>>> obj/ComputeMoa.o -c src/ComputeMoa.C
>>> In file included from src/HomePatchList.h:15:0,
>>> from src/PatchMap.h:11,
>>> from src/ComputeMoa.C:27:
>>> src/SortedArray.h: In member function ‘int
>>> SortedArray<Elem>::index(const Elem&)’:
>>> src/SortedArray.h:77:42: error: ‘found’ was not declared in this scope
>>> make: *** [obj/ComputeMoa.o] Error 1
>>> Using diff, it looks like "int found" was previously above "int
>>> isSorted" as a protected variable in the declaration of template <class
>>> Elem> class SortedArray: public SortableResizeArray<Elem> near the top of
>>> the old SortedArray.h. With the new update in SortedArray.h, "int found" is
>>> not declared as a class variable, but only as a local variable for a few
>>> functions. Re-adding "int found" seems to make the code build fine, and it
>>> seems to run this way too. However, the diff shows some significant
>>> differences between the old SortedArray.h and new SortedArray.h, so I'm
>>> unsure of any side effects by this "fix". Can anyone else confirm this?
>>> Michael J. M. Mazack
>>> Scientific Computation Program
>>> University of Minnesota
>>> Minneapolis, MN 55455
>>> E-mail: michael_at_mazack.org
>>> Web: http://mazack.org
>> Chris Harrison, Ph.D.
>> NIH Center for Macromolecular Modeling and Bioinformatics
>> Theoretical and Computational Biophysics Group
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>> http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078
>> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
> Michael J. M. Mazack
> Scientific Computation Program
> University of Minnesota
> Minneapolis, MN 55455
> E-mail: michael_at_mazack.org
> Web: http://mazack.org
-- Michael J. M. Mazack Scientific Computation Program University of Minnesota Minneapolis, MN 55455 E-mail: michael_at_mazack.org Web: http://mazack.org
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